A system and method for measuring the thickness of an ultra-thin multi-layer film on a substrate is disclosed. A physical model of an ultra-thin multilayer structure and Auger electron emission from the nano-multilayer structure is built. A mathematical model for the Auger Electron Spectroscopy (AES) measurement of the multilayer thin film thickness is derived according to the physical model. Auger electron spectroscopy (AES) is first performed on a series of calibration samples. The results are entered into the mathematical model to determine the parameters in the mathematical equation. The parameters may be calibrated by the correlation measurements of the alternate techniques. AES analysis is performed on the ultra-thin multi-layer film structure. The results are entered into the mathematical model and the thickness is calculated.